Leishmania major N-myristoyltransferase with bound myristoyl-CoA and inhibitor

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System.

Kersten, C.Fleischer, E.Kehrein, J.Borek, C.Jaenicke, E.Sotriffer, C.Brenk, R.

(2019) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00586
  • Primary Citation of Related Structures:  
    6EU5, 6EWF, 6F56, 6FZ2, 6FZ3, 6FZ5

  • PubMed Abstract: 

    A model system of two related enzymes with conserved binding sites, namely N -myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. Using a combination of computational and experimental tools, two different selectivity-determining features were identified. For some ligands, a change in side-chain flexibility appears to be responsible for selective inhibition. Remarkably, this was observed for residues orienting their side chains away from the ligands. For other ligands, selectivity is caused by interfering with a water molecule that binds more strongly to the off-target than to the target. On the basis of this finding, a virtual screen for selective compounds was conducted, resulting in three hit compounds with the desired selectivity profile. This study delivers a guideline on how to assess selectivity-determining features in proteins with conserved binding sites and to translate this knowledge into the design of selective inhibitors.

  • Organizational Affiliation

    Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase438Leishmania majorMutation(s): 0 
Gene Names: NMTLMJF_32_0080
Find proteins for Q4Q5S8 (Leishmania major)
Explore Q4Q5S8 
Go to UniProtKB:  Q4Q5S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4Q5S8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MYA

Download Ideal Coordinates CCD File 
C35 H62 N7 O17 P3 S
BXN (Subject of Investigation/LOI)
Query on BXN

Download Ideal Coordinates CCD File 
C [auth A]4-[3-[(8~{a}~{R})-3,4,6,7,8,8~{a}-hexahydro-1~{H}-pyrrolo[1,2-a]pyrazin-2-yl]propyl]-2,6-bis(chloranyl)-~{N}-methyl-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide
C23 H33 Cl2 N5 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
BXN Binding MOAD:  6EU5 Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.77α = 90
b = 90.59β = 114.141
c = 53.42γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description